1. Figure S1 (a) (b) Fig. S1. Hydroponics culture of Arabidopsis thaliana. (a) Illustration of the hydroponics system in the growth chamber. (b) close-up of a 4.5 l container with 5-weeks-old Arabidopsis thaliana Col-0 plants.

2. Figure S2 Ctrl 04h Ctrl 28h Ctrl 08h - Mg 04h -Mg 28h - Mg 08h A B AB AB AB A B A B A B Fig. S2. Experimental loop design with arrays hybridization. The design allowed the comparison between control fully supplied (Ctrl) and Mg deficient (-Mg) samples 04h, 08h and 28h after the removal of Mg from the nutrient solution, of two biological replicates (A,B). Each arrow represents one Agilent Arabidopsis3 (60-mer) oligonucleotide chips.

3. Figure S3 LILI Cluster R I Roots DOWN (cluster R I ) +7.7% *** +5.8% ** *** +15.8% +15.0% *** ** +4.1% Roots UP (cluster R II ) Leaves DOWN (cluster L I ) Leaves UP (cluster L II ) ** +8.1% *** +13.2% *** +11.5% *** +7.2% * +8.0% ** +5.4% *** +9.9% *** +8.8% *** +5.7% ** +3.5% Percentage of representation MIPS functional categories Fig. S3. MIPS functional distribution of the Mg deficiency regulated genes. Distribution of -Mg genes (black columns) in roots clusters R I (down-regulated by Mg depletion) and R II (up-regulated) and leaves clusters L I (down-regulated) and L II (up-regulated), and of the whole genome (white columns). In the graphics, the difference in representation compared to the whole genome categorization is also indicated in percentage above the bars for up to 5 categories showing the most important differences. Stars indicate significant differences: P<0.1 (*), P<0.01 (**), P<0.001 (***). Category 01: metabolism, 02: energy, 04: storage, 10: cell cycle and DNA processing, 11: transcription, 12: protein synthesis, 14: protein fate, 16: protein with binding function or cofactor requirement, 18: regulation of metabolism and protein function, 20: cellular transport, transport facilities and transport routes, 30: cellular communication/signal transduction mechanisms, 32: cell rescue, defense and virulence, 34: interaction with the environment, 36: systemic interaction with the environment, 40: cell fate, 41: development, 42: biogenesis of cellular components, 43: cell type differentiation, 45: tissue differentiation, 47: organ differentiation, 70: subcellular localization, 73: cell type localization, 77: organ localization, 99: unclassified proteins. Note that because cluster R I has several expected counts <5, the exact chances for overrepresentation in that cluster were calculated. Therefore, a Pearson chi square exact test was applied using StatXact v 8 (Cytel studio). No significant differences were found using this test.

4. Figure S4 Leaves At5g54190At2g40610At5g02760 At5g62040At3g02480At5g62490 At5g59310 Relative expression signal Roots Time of treatment At5g62040At2g46830At2g46790 At1g01060At5g51440 Relative expression signal 04h 08h 28h (a) (b) Fig. S4. Microarrays data reliability assessment. RT-qPCR assay of some genes differentially regulated by Mg deficiency in roots and leaves. Differential regulation of these genes by Mg deficiency was observed for at least one sampling point (see Tables S2, S3). n= 2 biological samples (from micro-arrays experiments) with 3 technical replicates ± SE. White column: control; black column: Mg deficiency.

5. Figure S5 (a ) 04h 08h 28h Ctrl 04h 08h 28h Treatmen t - N - K - P + NaCl + PEG Leave s Roots 04h 08h 28h Ctrl 04h 08h 28h Treatmen t NIA1/NIR 1 HAK5 PT2 KC I MAP 4 SAG21 HAK5 RNS 1 COR78/RD29 A MYB44 Ctrl-N-K-P +NaCl+PEG Ctrl-N-K-P +NaCl+PEG 18S 04h 08h 28h 04h 08h 28h (b) Fig. S5. Expression of genes markers for environmental stresses. (a) Semi-quantitative RT-PCR assay for specific genes markers of nitrate (-N), potassium (-K) and phosphate (-P) deficiencies and exposure to 50mM sodium chloride (+NaCl) and 10% w/v polyethylene glycol (+PEG). Equal loading between samples was indicated by equivalent 18S signals. (b) List of primers used for the sqPCR assay.